The operation is costing the state's taxpayers $36,000 (£22,000) and was ordered after Joshua Seater, 21, was caught on a security camera relieving himself in the pristine lake.
Health experts said the incident would not have caused any harm to people in the city of Portland, who are supplied with drinking water from the reservoir.
They said the average human bladder holds only six to eight ounces, and the urine would have been vastly diluted.
But David Shaff, an administrator at the Portland Water Bureau, defended the decision to empty the lake.
"There are people who will say it's an over reaction. I don't think so. I think what you have to deal with here is the 'yuck' factor," he said.